4HV4 | pdb_00004hv4

2.25 Angstrom resolution crystal structure of UDP-N-acetylmuramate--L-alanine ligase (murC) from Yersinia pestis CO92 in complex with AMP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2F00	PDB entry 2F00

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	295	Protein 7.4 mg/mL in 10 mM Tris-HCl pH8.3 0.5 M NaCl 5 mM BME, 1 mM ADP, 1 mM MgCl2 Crystallization: The PACT Suite (G7) - 0.2 M Sodium acetate 0.1 M Bis Tris propane pH 7.5 20% (w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.534	α = 90
b = 78.021	β = 90
c = 183.296	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD	Be Lenses	2012-10-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.25	30	99.3	0.093	17.8	6.9	45997	45997		-3	36.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.25	2.29	98.2		0.554	3.68	6.8	2259

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2F00	2.25	29.7	43511	43511	2317	99.28	0.18184	0.1795	0.18	0.22437	0.23	RANDOM	31.203

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-1.41			-1.1		2.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.795
r_dihedral_angle_4_deg	12.677
r_dihedral_angle_3_deg	10.753
r_scangle_it	4.48
r_scbond_it	2.881
r_dihedral_angle_1_deg	2.503
r_mcangle_it	1.691
r_angle_refined_deg	1.589
r_mcbond_it	0.915
r_angle_other_deg	0.867

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.795
r_dihedral_angle_4_deg	12.677
r_dihedral_angle_3_deg	10.753
r_scangle_it	4.48
r_scbond_it	2.881
r_dihedral_angle_1_deg	2.503
r_mcangle_it	1.691
r_angle_refined_deg	1.589
r_mcbond_it	0.915
r_angle_other_deg	0.867
r_mcbond_other	0.248
r_chiral_restr	0.094
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7099
Nucleic Acid Atoms
Solvent Atoms	282
Heterogen Atoms	54

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.